Occupancy in dynamic systems: accounting for multiple scales and false positives using environmental DNA to inform monitoring

Occupancy is an important metric to understand current and future trends in populations that have declined globally. In addition, occupancy can be an efficient tool for conducting landscape-scale and long-term monitoring. A challenge for occupancy monitoring programs is to determine the appropriate spatial scale of analysis and to obtain precise occupancy estimates for elusive species. We used a multi-scale occupancy model to assess occupancy of Columbia spotted frogs in the Great Basin, USA, based on environmental DNA (eDNA) detections. We collected three replicate eDNA samples at 220 sites across the Great Basin. We estimated and modeled ecological factors that described watershed and site occupancy at multiple spatial scales simultaneously while accounting for imperfect detection. Additionally, we conducted visual and dipnet surveys at all sites and used our paired detections to estimate the probability of a false positive detection for our eDNA sampling. We applied the estimated false positive rate to our multi-scale occupancy dataset and assessed changes in model selection. We had higher naïve occupancy estimates for eDNA (0.37) than for traditional survey methods (0.20). We estimated our false positive detection rate per qPCR replicate at 0.023 (95% CI: 0.016–0.033). When the false positive rate was applied to the multi-scale dataset, we did not observe substantial changes in model selection or parameter estimates. Conservation and resource managers have an increasing need to understand species occupancy in highly variable landscapes where the spatial distribution of habitat changes significantly over time due to climate change and human impact. A multi-scale occupancy approach can be used to obtain regional occupancy estimates that can account for spatially dynamic differences in availability over time, especially when assessing potential declines. Additionally, this study demonstrates how eDNA can be used as an effective tool for improved occupancy estimates across broad geographic scales for long-term monitoring.     

Responses of nitrogen and phosphorus resorption from leaves and branches to long-term nitrogen deposition in a Chinese fir plantation

为了解森林养分内循环对全球变化的响应, 基于长期模拟氮沉降试验, 研究了杉木(Cunninghamia lanceolata)人工林不同龄级(一年生、二年生和衰老)叶和枝的氮(N)、磷(P)养分分配及其再吸收特征, 并分析了不同模拟N沉降处理时间(7年和14年)杉木叶N、P养分再吸收差异。在12年生杉木中开展模拟N沉降试验, 以尿素(CO(NH₂)₂)为N源, 设N0、N1、N2和N3 4个处理水平, 施氮量分别为0、60、120和240 kg·hm ^-2·a ^-1, 每个处理重复3次。结果表明: (1)叶和枝在衰老过程中碳(C)、N和P含量逐渐降低, 且叶的C、N和P含量比枝高; N含量大小依次为一年生叶>二年生叶>衰老叶>一年生枝>二年生枝>衰老枝, 且N3 > N2 > N1 > N0, 而C:N则呈现相反的趋势; 衰老器官的C:N、C:P、N:P比新鲜器官高; N沉降增加了不同龄级叶和枝(除二年生叶外)的N、N:P和C:P, 但降低了P和C:N。(2)叶和枝的N、P养分再吸收率(RE_N、RE_P)随龄级的增加至衰老有规律地递减, 且RE_P > RE_N; 受长期N沉降的影响, RE_N叶(28.12%) <枝(30.00%), 而RE_P则为叶(45.82%) >枝(30.42%); 杉木叶和枝N:P与RE_N:RE_P之间存在极显著的线性相关关系。(3)随N沉降处理时间的增加, 叶RE_N呈降低态势, 各处理(N1、N2和N3)分别降低了9.85%、3.17%和11.71%; 而RE_P则明显上升, 分别增加了71.98%、42.25%和9.60%。研究结果表明: 不同器官、不同龄级的养分再吸收率随氮沉降处理的水平、处理时间而所有不同; RE_N:RE_P与N:P之间存在紧密关系。     

Determination of free amino acids in burley tobacco by high performance liquid chromatography

A reversed-phase high performance liquid chromatographic method was developed for determining free amino acids in burley tobacco. The test was done by OPA/3-mercaptopropionic acid as the pre-column derivatizing reagent. Chromatographic column was Elitte C¹⁸ column (4.6 mm × 250 mm i.d., 5 μm). Mobile phase A was 18 mol/l NaAc (pH7.2) including 0.002%(v/v) triethylamine and 0.3%(v/v) furanidine. Mobile phase B was 100 mol/l NaAc (pH7.2)–acetonitrile–methanol (v/v = 1:2:2). The column temperature was 40 °C and the flow rate was 1.0 ml/min. The fluorescence detector was used with 350 nm excitation wave length and 450 nm emission wave length. The average recoveries of the method ranged from 95.3–100.7% with the relative standard deviation of 2.32–9.24%. The method is simple, accurate and has good repeatability. The results of the determination of seventeen kinds of free amino acids in burley leaves were produced by the way of different ratios of cake fertilizer and inorganic fertilizer. The results show that Aspartic acid has the highest content however ratio of cake fertilizer and inorganic fertilizer. The contents of most of the free amino acids are increased and then gradually decreased with the increase in organic manure. The contents of most of the free amino acids are very close at 15:85% ratio and 30:70% ratio of cake fertilizer and inorganic fertilizer. The total amount of free amino acids is the highest at 30:70% ratio of cake fertilizer and inorganic fertilizer. Considering comprehensively, the quality of burley leaves is the best at 30:70% ratio of cake fertilizer and inorganic fertilizer.     

The ecological and evolutionary significance of frost in the context of climate change

The effects that below-freezing temperature (frost) can have at times of year when it is unusual are an interesting ecological phenomenon that has received little attention. The physiological consequence of formation of ice crystals in plant tissue is often death of the plants, or at least of sensitive parts that can include flower buds, ovaries, and leaves. The loss of potential for sexual reproduction can have long-lasting effects on the demography of annuals and long-lived perennials, because the short-term negative effects of frosts can result in longer-term benefits through lowered populations of seed predators. The loss of host plants can have dramatic consequences for herbivores, even causing local extinctions, and the loss of just flowers can also affect populations of seed predators and their parasitoids. Frosts can cause local extinctions and influence the geographical distribution of some species. The potential for global climate change to influence the frequency and distribution of frost events is uncertain, but it seems likely that they may become more frequent in some areas and less frequent in others.     

Performance and efficiency of a yeast biofilter for the treatment of a Nigerian fertilizer plant effluent

A biofilter composed of yeasts and cassava peel was used to detoxify fertilizer plant effluent. The biological oxygen demand was reduced on treatment from a range of 1200–1400 mg/l to a range 135–404 mg/l. The ammonia-nitrogen (NH₃–N) and nitrate-nitrogen (NO₃–N) were reduced after treatment from 1000 to 10 mg/l and from 100 to 17.6 mg/l, respectively. The biofilter is simple and easy to handle with high efficiency of 98%.     

An evaluation of carbon disulphide as a sulphur fertilizer and as a nitrification inhibitor

There was little release of extractable SO₄-S during four weeks from CS₂ applied by injecting into two S-deficient soils. In this incubation experiment, the rate of CS₂ was 30 μg S g⁻, placement was injection at 9 cm depth, soil temperature was 20°C, and soil moisture tension was 33 kPa. The yield of barley forage after seven weeks in the greenhouse showed only small increases from 10 or 30 μg S g⁻¹ of CS₂ as compared to Na₂SO₄, on the two soils. While CS₂ supplied little plant available S in the short term, it was an effective inhibitor of nitrification. In the laboratory, or in the field, the injection of CS₂ (with N fertilizers) at a point 9 cm into the soils either stopped or reduced nitrification. In one laboratory experiment, 35 μg of CS₂ g⁻¹ of soil with urea reduced nitrification for at least four weeks; and in another experiment 20 μg of CS₂ g⁻¹ of soil with aqua NH₃ nearly or completely inhibited nitrification at 20 days. In two field experiments, 3 and 12 μg of CS₂ g⁻¹ of soil (or 6 and 24 kg ha⁻¹) with aqua NH₃ inhibited nitrification from October to the subsequent May. In addition, CS₂ reduced the amount of ammonium produced from the soil N, both in these two field experiments and in the laboratory experiments. That is to say, CS₂ injected at a point, inhibited both nitrification and ammonification. In other field experiments, CS₂ at a rate of 10 kg ha⁻¹ was injected in bands 9 cm deep with urea in October, and by May there was still reduced nitrification. Less than half of the fall-applied urea alone was recovered as mineral N, but with the application of CS₂ the recovery was increased to three-quarters. The yield and N uptake of barley grain was increased where fall-applied banded urea or aqua NH₃ received banded CS₂, (NH₄)₂CS₃, or K₂CS₃. The average increase in yield from fall-applied fertilizer, from inhibitor with fall-applied fertilizer, and from spring-applied fertilizer was 800, 1370, and 1900 kg ha⁻¹, respectively. In the same order, the apparent % recovery of fertilizer N in grain was 24, 42, and 60.     

Prediction of yield in the Rothamsted Park Grass Experiment by Ellenberg indicator values

Abstract. The Rothamsted Park Grass Experiment was established in 1856, with experimental plots subjected to annual applications of fertilizer and twice-yearly cutting of hay. There were two major responses to fertilizer, one reflecting high ammonium-nitrogen and increased acidity and the other reflecting high herbage yield without increased acidity. We calculated mean Ellenberg indicator values for N (nitrogen) and R (soil reaction) for the hay harvested between 1948 and 1975, using both unweighted and abundance-weighted means. Plot Ellenberg values were compared with herbage yield and with fertilizer application rates and published soil data. Annual yield of hay varied from 1.5 to 7.4 t/ha and was well predicted by the unweighted mean Ellenberg N-values (r = 0.91). Relatively large negative residuals from the relationship were found in plots whose soil combined low K and low pH. Soil pH was poorly predicted by the unweighted mean R-value, but showed a moderately good relation with weighted mean R (r = 0.73). The fact that Ellenberg N-values correlated better with yield than with applied nitrogen suggests that they might rather be called productivity values.     

Effects of additional illumination and fertilization on seasonal changes in fine-scale grassland community structure

Abstract. Fine-scale structure of a species-rich grassland was examined for seasonal changes caused by manipulated changes in the availability of above and below-ground resources (additional illumination with the help of mirrors and fertilization) in a field experiment. If changes induced by fertilization — which are expected to lead to a reduction in small-scale diversity —are due to intensified light competition, they should be compensated for by additional light input. Permanent plots of 40 cm × 40 cm were sampled by the point quadrat method at three angles (60°, 90° and 120° from the horizontal North-South direction), using a laser beam to position the quadrats, in early July and early September. The applied treatments did not cause apparent changes in plant leaf orientation. The degree of spatial aggregation of biomass increased seasonally in fertilized, non-illuminated plots: greater productivity at a constant light supply led to a faster growth rate of potentially dominant species, as compared to the subordinate ones. Additional illumination mitigated this effect of fertilization, indicating that the observed changes in biomass aggregation were due to increased light competition. There was a considerable seasonal decrease of variance ratio (ratio of observed variance of richness at a point and variance expected at random) in fertilized only and in illuminated only plots. In fertilized plots this was due to the positive relationship between biomass aggregation and expected variance of richness. Biomass constancy occurs to be inversely related to deficit in variance of richness. In illuminated plots, in contrast, only the observed variance of richness decreased seasonally, indicating a more uniform use of space by different species. Evidently, a deficit in variance of richness can be caused by drastically different processes, showing that the variance ratio statistic may not have a significant explanatory value in fine-scale community studies.